VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 08 2015 - 14:06:14 CST
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There isn't a pre-written script to do what you ask included in VMD,
but I'm sure you could write one. I assume that you're using NAMDEnergy
for your energy evaluation? Keep in mind that any calculation involving all
pairs has quadratic runtime and will be very slow for anything other than
a very small system, as well as generating a lot of output.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Tue, Dec 08, 2015 at 11:48:04AM +0300, elena ermakova wrote:
> Hello,
>
>
>
> I would really appreciate if anyone can provide some input to the
> following question:
>
> VMD is able to calculate interaction energy between any pair of residues
> along the trajectory.
>
> Question is:
> Is any script which allow to calculate the interaction energies between
> ALL pairs of residues ( may be in cycle) and save them to file or files?
>
> Thank you very much.
>
> Elena
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/
- Next message: Georgia Tsagkaropoulou: "[lammps-users] NPT/ Missing bonds / atoms & atom overlap"
- Previous message: Joaquim Rui de Castro Rodrigues: "RE: Defining space coordinates for multiple structures"
- In reply to: elena ermakova: "residue-residue interaction energy"
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